Differences

This shows you the differences between two versions of the page.

--- guppy-software [2022/05/24 09:00] – aorth
+++ guppy-software [2022/05/24 10:00] – aorth
@@ Line 32: / Line 32: @@
 Run some test data using fourteen CPUs:
-<code>$ cd /var/scratch
+<code>$ mkdir -p /var/scratch/aorth/2022-05-24-guppy
-$ mkdir -p /var/scratch/aorth/2021-07-01-guppy
+$ cd /var/scratch/aorth/2022-05-24-guppy
 $ wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Data_Group1.tar.gz
-$ tar xf Data_Group1.tar.gz -C /var/scratch/aorth/2021-07-01-guppy
+$ tar xf Data_Group1.tar.gz
-$ guppy_basecaller --compress_fastq -i /var/scratch/aorth/2021-07-01-guppy/data/fast5_tiny/ -s /var/scratch/aorth/2021-07-01-guppy/data/basecall_tiny/ --cpu_threads_per_caller 14 --num_callers 1 -c dna_r9.4.1_450bps_hac.cfg
+$ guppy_basecaller --compress_fastq -i data/fast5_tiny/ -s data/basecall_tiny/ --cpu_threads_per_caller 14 --num_callers 1 -c dna_r9.4.1_450bps_hac.cfg
 ...
-Caller time: 208271 ms, Samples called: 27619692, samples/s: 132614</code>
+Caller time: 3281435 ms, Samples called: 27619692, samples/s: 8416.96</code>
 Run some test data using a GPU (currently only on compute06):
-<code>$ guppy_basecaller --device "cuda:0" --compress_fastq -i /var/scratch/aorth/2021-07-01-guppy/data/fast5_tiny/ -s /var/scratch/aorth/2021-07-01-guppy/data/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg
+<code>$ guppy_basecaller --device "cuda:0" --compress_fastq -i data/fast5_tiny/ -s /var/scratch/aorthdata/basecall_tiny/ -c dna_r9.4.1_450bps_hac.cfg
 ...
-Caller time: 2994 ms, Samples called: 27619692, samples/s: 9.22501e+06</code>
+Caller time: 4366 ms, Samples called: 27619692, samples/s: 6.32609e+06</code>